The effects of the chemical nature of an interface are one of the key parameters which can affect self-assembly and rheological behavior. To date, several studies have reported self-assembled structures and rheological behaviors in the development of various functional materials. In this study, we investigated the self-assembly and viscosity behavior of aqueous surfactant solutions confined in three types of Janus amphiphilic nanotubes (JANTs), which have two, four, and eight sequential domains, respectively, using molecular simulation. We found that the viscosity behavior depends on the surfactant concentration and the chemical nature of the wall surface. For instance, although the concentration levels of the surfactants are the same (c = 10%), completely different viscosity behaviors were observed in the two sequential domains (Newtonian-like) and the four and eight sequential domains (strong shear-thinning) of the JANTs. Our simulations demonstrated how the rheological properties of aqueous surfactant solutions, including viscosity and velocity profiles, can be controlled by the chemical nature of the JANT wall surface, effect of confinement, and their self-assembly structures. Considering the foregoing, we hope that our study offers new knowledge on nanofluid systems.